Kari Branham, Hiroko Matsui, Pooja Biswas, Aditya A. Guru, Michael Hicks, John J. Suk, He Li, David Jakubosky, Tao Long, Amalio Telenti, Naoki Nariai, John R. Heckenlively, Kelly A. Frazer, Paul A. Sieving, Radha Ayyagari | Physiol Genomics | 2016 Dec 13 | doi/full/10.1152/physiolgenomics.00101.2016
Abstract
While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40–50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of IRD in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10. Sequence reads were aligned to hg19 using BWA-MEM and variant calling was performed with Genome Analysis Toolkit. The called variants were annotated with SnpEff v4.11, PolyPhen v2.2.2, and CADD v1.3. Copy number variations were called using Genome STRiP (svtoolkit 2.00.1611) and SpeedSeq software. Variants were filtered to detect rare potentially deleterious variants segregating with disease. Candidate variants were validated by dideoxy sequencing. Clinical evaluation revealed typical adolescent-onset recessive retinitis pigmentosa (arRP) in affected members. WGS identified about 4 million variants in each individual. Two rare and potentially deleterious compound heterozygous variants p.Arg281Cys and p.Arg487* were identified in the gene ATP/GTP binding protein like 5 (AGBL5) as likely causal variants. No additional variants in IRD genes that segregated with disease were identified. Mutation analysis confirmed the segregation of these variants with the IRD in the pedigree. Homology models indicated destabilization of AGBL5 due to the p.Arg281Cys change. Our findings establish the involvement of mutations in AGBL5 in RP and validate the WGS variant filtering pipeline we designed.
Inherited retinal degenerations (IRD) are a group of genetically and phenotypically heterogeneous diseases that result in irreversible loss of vision. So far, involvement of more than 250 genes in causing IRD has been reported (RetNet) (27). However, mutations in these genes are estimated to contribute to only about 50–60% of cases and the underlying cause of IRD in the remaining is unknown. The availability of whole exome sequencing has allowed researchers to screen large cohorts of patients affected with IRD and to identify mutations in known IRD genes or potentially pathogenic variants in novel genes. However, the pathogenic changes found in novel genes are often observed only in one or two small pedigrees, leaving these genes only as possible candidates for IRD. Since exome sequencing methodology does not support the exclusion of all known IRD genes, additional evidence is needed to confirm the involvement of these novel candidates.
ABGL5 is one of the genes reported as a candidate for recessive retinal degeneration. Potentially deleterious variants in AGBL5 have been reported to segregate with recessive IRD in two small pedigrees in two independent studies, one from a Saudi population and another from a Turkish population by sequencing whole exomes. The current study describes whole genome sequencing (WGS) analysis of a clinically well-characterized pedigree with a presumed recessive IRD. Absence of mutations including large sequence rearrangements in coding or putative regulatory regions of known IRD genes and identification of rare and deleterious compound heterozygous mutations in the AGBL5 gene segregating with disease in our study pedigree confirm the involvement this gene in IRD pathology.
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